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Westall F, Brack A, Fairén AG, Schulte MD. Setting the geological scene for the origin of life and continuing open questions about its emergence. FRONTIERS IN ASTRONOMY AND SPACE SCIENCES 2023; 9:1095701. [PMID: 38274407 PMCID: PMC7615569 DOI: 10.3389/fspas.2022.1095701] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
The origin of life is one of the most fundamental questions of humanity. It has been and is still being addressed by a wide range of researchers from different fields, with different approaches and ideas as to how it came about. What is still incomplete is constrained information about the environment and the conditions reigning on the Hadean Earth, particularly on the inorganic ingredients available, and the stability and longevity of the various environments suggested as locations for the emergence of life, as well as on the kinetics and rates of the prebiotic steps leading to life. This contribution reviews our current understanding of the geological scene in which life originated on Earth, zooming in specifically on details regarding the environments and timescales available for prebiotic reactions, with the aim of providing experimenters with more specific constraints. Having set the scene, we evoke the still open questions about the origin of life: did life start organically or in mineralogical form? If organically, what was the origin of the organic constituents of life? What came first, metabolism or replication? What was the time-scale for the emergence of life? We conclude that the way forward for prebiotic chemistry is an approach merging geology and chemistry, i.e., far-from-equilibrium, wet-dry cycling (either subaerial exposure or dehydration through chelation to mineral surfaces) of organic reactions occurring repeatedly and iteratively at mineral surfaces under hydrothermal-like conditions.
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Affiliation(s)
| | - André Brack
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
| | - Alberto G. Fairén
- Centro de Astrobiología (CAB, CSIC-INTA), Madrid, Spain
- Cornell University, Ithaca, NY, United States
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Stolar T, Grubešić S, Cindro N, Meštrović E, Užarević K, Hernández JG. Mechanochemical Prebiotic Peptide Bond Formation*. Angew Chem Int Ed Engl 2021; 60:12727-12731. [PMID: 33769680 DOI: 10.1002/anie.202100806] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/11/2021] [Indexed: 12/15/2022]
Abstract
The presence of amino acids on the prebiotic Earth, either stemming from endogenous chemical routes or delivered by meteorites, is consensually accepted. Prebiotically plausible pathways to peptides from inactivated amino acids are still unclear as most oligomerization approaches rely on thermodynamically disfavored reactions in solution. Now, a combination of prebiotically plausible minerals and mechanochemical activation enables the oligomerization of glycine at ambient temperature in the absence of water. Raising the reaction temperature increases the degree of oligomerization concomitantly with the formation of a commonly unwanted cyclic glycine dimer (DKP). However, DKP is a productive intermediate in the mechanochemical oligomerization of glycine. The findings of this research show that mechanochemical peptide bond formation is a dynamic process that provides alternative routes towards oligopeptides and establishes new synthetic approaches for prebiotic chemistry.
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Affiliation(s)
- Tomislav Stolar
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
| | - Saša Grubešić
- Xellia Pharmaceuticals, Slavonska avenija 24/6, 10000, Zagreb, Croatia
| | - Nikola Cindro
- Department of Organic Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - Ernest Meštrović
- Xellia Pharmaceuticals, Slavonska avenija 24/6, 10000, Zagreb, Croatia
| | - Krunoslav Užarević
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
| | - José G Hernández
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
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Stolar T, Grubešić S, Cindro N, Meštrović E, Užarević K, Hernández JG. Mechanochemical Prebiotic Peptide Bond Formation**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tomislav Stolar
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| | - Saša Grubešić
- Xellia Pharmaceuticals Slavonska avenija 24/6 10000 Zagreb Croatia
| | - Nikola Cindro
- Department of Organic Chemistry Faculty of Science University of Zagreb Horvatovac 102a 10000 Zagreb Croatia
| | - Ernest Meštrović
- Xellia Pharmaceuticals Slavonska avenija 24/6 10000 Zagreb Croatia
| | - Krunoslav Užarević
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| | - José G. Hernández
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
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Martínez-Bachs B, Rimola A. Prebiotic Peptide Bond Formation Through Amino Acid Phosphorylation. Insights from Quantum Chemical Simulations. Life (Basel) 2019; 9:life9030075. [PMID: 31527465 PMCID: PMC6789625 DOI: 10.3390/life9030075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/08/2019] [Accepted: 09/09/2019] [Indexed: 12/11/2022] Open
Abstract
Condensation reactions between biomolecular building blocks are the main synthetic channels to build biopolymers. However, under highly diluted prebiotic conditions, condensations are thermodynamically hampered since they release water. Moreover, these reactions are also kinetically hindered as, in the absence of any catalyst, they present high activation energies. In living organisms, in the formation of peptides by condensation of amino acids, this issue is overcome by the participation of adenosine triphosphate (ATP), in which, previous to the condensation, phosphorylation of one of the reactants is carried out to convert it as an activated intermediate. In this work, we present for the first time results based on density functional theory (DFT) calculations on the peptide bond formation between two glycine (Gly) molecules adopting this phosphorylation-based mechanism considering a prebiotic context. Here, ATP has been modeled by a triphosphate (TP) component, and different scenarios have been considered: (i) gas-phase conditions, (ii) in the presence of a Mg2+ ion available within the layer of clays, and (iii) in the presence of a Mg2+ ion in watery environments. For all of them, the free energy profiles have been fully characterized. Energetics derived from the quantum chemical calculations indicate that none of the processes seem to be feasible in the prebiotic context. In scenarios (i) and (ii), the reactions are inhibited due to unfavorable thermodynamics associated with the formation of high energy intermediates, while in scenario (iii), the reaction is inhibited due to the high free energy barrier associated with the condensation reactions. As a final consideration, the role of clays in this TP-mediated peptide bond formation route is advocated, since the interaction of the phosphorylated intermediate with the internal clay surfaces could well favor the reaction free energies.
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Affiliation(s)
- Berta Martínez-Bachs
- Department de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Albert Rimola
- Department de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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Tabacchi G, Fabbiani M, Mino L, Martra G, Fois E. The Case of Formic Acid on Anatase TiO 2 (101): Where is the Acid Proton? Angew Chem Int Ed Engl 2019; 58:12431-12434. [PMID: 31310450 DOI: 10.1002/anie.201906709] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Indexed: 01/20/2023]
Abstract
Carboxylic-acid adsorption on anatase TiO2 is a relevant process in many technological applications. Yet, despite several decades of investigations, the acid-proton localization-either on the molecule or on the surface-is still an open issue. By modeling the adsorption of formic acid on top of anatase(101) surfaces, we highlight the formation of a short strong hydrogen bond. In the 0 K limit, the acid-proton behavior is ruled by quantum delocalization effects in a single potential well, while at ambient conditions, the proton undergoes a rapid classical shuttling in a shallow two-well free-energy profile. This picture, supported by agreement with available experiments, shows that the anatase surface acts like a protecting group for the carboxylic acid functionality. Such a new conceptual insight might help rationalize chemical processes involving carboxylic acids on oxide surfaces.
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Affiliation(s)
- Gloria Tabacchi
- Department of Science and High Technology, University of Insubria and INSTM, via Valleggio 9, I-22100, Como, Italy
| | - Marco Fabbiani
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centre, University of Torino, via P. Giuria 7, I-10125, Torino, Italy
| | - Lorenzo Mino
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centre, University of Torino, via P. Giuria 7, I-10125, Torino, Italy
| | - Gianmario Martra
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centre, University of Torino, via P. Giuria 7, I-10125, Torino, Italy
| | - Ettore Fois
- Department of Science and High Technology, University of Insubria and INSTM, via Valleggio 9, I-22100, Como, Italy
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Tabacchi G, Fabbiani M, Mino L, Martra G, Fois E. The Case of Formic Acid on Anatase TiO
2
(101): Where is the Acid Proton? Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906709] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Gloria Tabacchi
- Department of Science and High TechnologyUniversity of Insubria and INSTM via Valleggio 9 I-22100 Como Italy
| | - Marco Fabbiani
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centreUniversity of Torino via P. Giuria 7 I-10125 Torino Italy
| | - Lorenzo Mino
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centreUniversity of Torino via P. Giuria 7 I-10125 Torino Italy
| | - Gianmario Martra
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centreUniversity of Torino via P. Giuria 7 I-10125 Torino Italy
| | - Ettore Fois
- Department of Science and High TechnologyUniversity of Insubria and INSTM via Valleggio 9 I-22100 Como Italy
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Pantaleone S, Ugliengo P, Sodupe M, Rimola A. When the Surface Matters: Prebiotic Peptide-Bond Formation on the TiO 2 (101) Anatase Surface through Periodic DFT-D2 Simulations. Chemistry 2018; 24:16292-16301. [PMID: 30212609 DOI: 10.1002/chem.201803263] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Indexed: 12/13/2022]
Abstract
The mechanism of the peptide-bond formation between two glycine (Gly) molecules has been investigated by means of PBE-D2* and PBE0-D2* periodic simulations on the TiO2 (101) anatase surface. This is a process of great relevance both in fundamental prebiotic chemistry, as the reaction univocally belongs to one of the different organizational events that ultimately led to the emergence of life on Earth, as well as from an industrial perspective, since formation of amides is a key reaction for pharmaceutical companies. The efficiency of the surface catalytic sites is demonstrated by comparing the reactions in the gas phase and on the surface. At variance with the uncatalyzed gas-phase reaction, which involves a concerted nucleophilic attack and dehydration step, on the surface these two steps occur along a stepwise mechanism. The presence of surface Lewis and Brönsted sites exerts some catalytic effect by lowering the free energy barrier for the peptide-bond formation by about 6 kcal mol-1 compared to the gas-phase reaction. Moreover, the co-presence of molecules acting as proton-transfer assistants (i.e., H2 O and Gly) provide a more significant kinetic energy barrier decrease. The reaction on the surface is also favorable from a thermodynamic standpoint, involving very large and negative reaction energies. This is due to the fact that the anatase surface also acts as a dehydration agent during the condensation reaction, since the outermost coordinatively unsaturated Ti atoms strongly anchor the released water molecules. Our theoretical results provide a comprehensive atomistic interpretation of the experimental results of Martra et al. (Angew. Chem. Int. Ed. 2014, 53, 4671), in which polyglycine formation was obtained by successive feedings of Gly vapor on TiO2 surfaces in dry conditions and are, therefore, relevant in a prebiotic context envisaging dry and wet cycles occurring, at mineral surfaces, in a small pool.
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Affiliation(s)
- Stefano Pantaleone
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS), Inter-Departmental centre, Università degli Studi di Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
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8
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McKee AD, Solano M, Saydjari A, Bennett CJ, Hud NV, Orlando TM. A Possible Path to Prebiotic Peptides Involving Silica and Hydroxy Acid‐Mediated Amide Bond Formation. Chembiochem 2018; 19:1913-1917. [DOI: 10.1002/cbic.201800217] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Aaron D. McKee
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology 901 Atlantic Drive Atlanta GA 30332 USA
| | - Martin Solano
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology 901 Atlantic Drive Atlanta GA 30332 USA
| | - Andrew Saydjari
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
| | - Christopher J. Bennett
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
- Department of Physics University of Central Florida Physical Sciences Bldg. 430 4111 Libra Drive Orlando FL 32816 USA
| | - Nicholas V. Hud
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology 901 Atlantic Drive Atlanta GA 30332 USA
| | - Thomas M. Orlando
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology 901 Atlantic Drive Atlanta GA 30332 USA
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9
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Iron(III) Oxide Nanoparticles as Catalysts for the Formation of Linear Glycine Peptides. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201601296] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Forsythe JG, Yu SS, Mamajanov I, Grover MA, Krishnamurthy R, Fernández FM, Hud NV. Ester-Mediated Amide Bond Formation Driven by Wet-Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503792] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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11
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Forsythe JG, Yu SS, Mamajanov I, Grover MA, Krishnamurthy R, Fernández FM, Hud NV. Ester-Mediated Amide Bond Formation Driven by Wet-Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth. Angew Chem Int Ed Engl 2015. [PMID: 26201989 PMCID: PMC4678426 DOI: 10.1002/anie.201503792] [Citation(s) in RCA: 205] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Although it is generally accepted that amino acids were present on the prebiotic Earth, the mechanism by which α-amino acids were condensed into polypeptides before the emergence of enzymes remains unsolved. Here, we demonstrate a prebiotically plausible mechanism for peptide (amide) bond formation that is enabled by α-hydroxy acids, which were likely present along with amino acids on the early Earth. Together, α-hydroxy acids and α-amino acids form depsipeptides—oligomers with a combination of ester and amide linkages—in model prebiotic reactions that are driven by wet–cool/dry–hot cycles. Through a combination of ester–amide bond exchange and ester bond hydrolysis, depsipeptides are enriched with amino acids over time. These results support a long-standing hypothesis that peptides might have arisen from ester-based precursors.
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Affiliation(s)
- Jay G Forsythe
- NSF/NASA Center for Chemical Evolution (USA).,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA (USA)
| | - Sheng-Sheng Yu
- NSF/NASA Center for Chemical Evolution (USA).,School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA (USA)
| | - Irena Mamajanov
- NSF/NASA Center for Chemical Evolution (USA).,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA (USA)
| | - Martha A Grover
- NSF/NASA Center for Chemical Evolution (USA).,School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA (USA)
| | - Ramanarayanan Krishnamurthy
- NSF/NASA Center for Chemical Evolution (USA). .,Department of Chemistry, The Scripps Research Institute, La Jolla, CA (USA).
| | - Facundo M Fernández
- NSF/NASA Center for Chemical Evolution (USA). .,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA (USA).
| | - Nicholas V Hud
- NSF/NASA Center for Chemical Evolution (USA). .,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA (USA).
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Fox S, Dalai P, Lambert JF, Strasdeit H. Hypercondensation of an amino acid: synthesis and characterization of a black glycine polymer. Chemistry 2015; 21:8897-904. [PMID: 25933438 DOI: 10.1002/chem.201500820] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Indexed: 12/24/2022]
Abstract
A granular material was obtained by thermal polymerization of glycine at 200 °C. It has been named "thermomelanoid" because of its strikingly deep-black color. The polymerization process is mainly a dehydration condensation leading to conventional amide bonds, and also CC double bonds that are formed from CO and CH2 groups ("hypercondensation"). Spectroscopic data, in particular from (13) C and (15) N solid-state cross-polarization magic angle spinning (CP-MAS) NMR spectra, suggest that the black color is due to (cross-)conjugated CC, CO, and NH groups. Small glycine peptides, especially triglycine, appear to be key intermediates in the formation of the thermomelanoid. This has been concluded by comparing the thermal behavior of glyn homopeptides (n=2-6) and glycine. The glycine polymerization was accompanied by the formation of small amounts of byproducts. Notably, a few percent of alanine and aspartic acid could be detected in the polymer. By using (13) C-labeled glycine, it was shown that these two amino acids formed through a common pathway, namely CαCα bond formation between glycine molecules. The thermomelanoid is hydrolyzed by strong acids and bases at room temperature, forming brown solutions.
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Affiliation(s)
- Stefan Fox
- Institut für Chemie, Universität Hohenheim, Garbenstr. 30, 70599 Stuttgart (Germany)
| | - Punam Dalai
- Institut für Chemie, Universität Hohenheim, Garbenstr. 30, 70599 Stuttgart (Germany)
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface, UMR CNRS 7197, Université Pierre et Marie Curie, Paris 6, 4 place Jussieu, 75252 Paris Cedex 05 (France)
| | - Henry Strasdeit
- Institut für Chemie, Universität Hohenheim, Garbenstr. 30, 70599 Stuttgart (Germany).
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